Plot hole: Scully's statement that she was 23 when she wrote her senior thesis in college throws off her timeline of college, med school, residency, FBI Academy, Quantico teaching assignment for two years, and X-Files assignment at 28. Her undergraduate degree in Physics should have been completed when she was 20 or 21 to allow at least 4 or 5 years for her medical training. (00:41:35)
Plot hole: Agent Spender watches in horror as Alex Krycek stabs the neck of an alien directly in front of him and the usual bubbling green blood spills out. In every other instance of a human being in such close proximity to the green blood, the person has immediately taken a painful reaction to the substance, including severe damage to the eyes. Spender however is completely unaffected, as is Krycek, who was also close enough to feel the effects.
Plot hole: When Scully enters the game room after the game has shut off and the Lone Gunman are there but Mulder is missing. She is told that the only way in/out is from the door she came in. Later we find out that the bay that players use to enter the game is at the other end of the room and not conected to the door Scully used. So how did Mulder and Scully enter the game from the bay when the game was running?
Plot hole: The ability of the Faceless Rebels to impersonate other people completely defies logic. For one, when impersonating someone, the Faceless Rebel is able to speak despite the fact that they mutilate their own mouths shut. Secondly, as can be seen in many instances when a person is being attacked by a Faceless Rebel, the face of the person they are impersonating is merely a skin mask that can easily be pulled off. If the face of the person they are impersonating is just a mask, then any time a Faceless Rebel speaks you should be able to see their true face through the open mouth of the skin mask. Additionally, the face of the person being impersonated being a mask would also preclude the Faceless Rebel from blinking or moving the mask's eyes (similarly they mutilate their own eyes shut, so the eyes of the skin mask can't be their own).
Plot hole: At his arrival at the Arecibo observatory, Mulder crushes the padlock on the door leading to the control building, and then he finds the native man, Jorge, in the toilet, who hid himself in the building. There's no way Jorge could enter the building and also lock himself in there with the padlock. (00:17:45)
Plot hole: At The End of the episode Scully handcuffs Tooms to the bathtub and Mulder says "he's not gonna get his quota this year" and Tooms seemingly accepts his capture. Given that he can stretch his whole body (and as specifically shown in the episode, his hands/fingers) couldn't Tooms have escaped from the handcuffs?
Plot hole: When Mulder and Scully are going to the town/city where the disappearances took place Scully says they should stop so she can walk the dog. Mulder says OK because he has to ask for directions yet the next scene we see is Mulder and Scully interviewing Dr. Faraday. How did they find him if they didn't know where they were?. And after that we see them at a store where they do ask for directions. (00:08:30)
Plot hole: Mulder is pulled from the escape hole previously dug by the hybrid aliens to escape the train car. When they pull him out they show alien bodies remaining in the hole. Mulder never revisits the train car despite knowing there's a high probability of finding hard evidence, in this case some actual bodies. There's no way Mulder would just assume there's no evidence remaining there and not go have a look for himself. Same goes for Cancerman who thought he had destroyed the evidence.
Plot hole: On the phone, Scully asks for the report on her sister to be sent to the San Diego F.B.I field office (since she is visiting her brother and his wife and so is not in Washington), but the package is sent to her brother's home. Even if 'Danny,' whom she asks for the file, decided to be helpful and send it directly to her, her brother's address is not likely to be the one in her personal file, plus she didn't mention that that's where she'd be staying.
Plot hole: When Arthur wakes up on the bus, he sees an alien reflection in the window beside Josh, but it's not possible that the reflection could be seen at all - especially from the angle that Arthur first sees it - considering how much of the pillow is covering both Josh's face and the window. The pillow extends past Josh's face so he could lean on it as cushioning against the window, but somehow Arthur sees a full facial reflection.
Plot hole: After Exley has gotten up after being hit by the ball, Dales notices green alien blood inside the glove where the back of Exley's head was resting. However, Exley was hit in the face, not the back of the head; not only was there no bleeding face wound while he was on the ground, but the glove was clean when Exley first gets up.
Plot hole: When Arthur looks closely at the green alien blood on the baseball glove, he has no reaction to it, despite the continuous pattern in the show about the blood being incredibly toxic to humans, even from a distance. It should have badly hurt his eyes at the least.
Plot hole: It is virtually impossible that such a conspiracy-experienced, cautious, and wise person as the Second Elder would be so naive and careless to just let the "Dr. Openshaw" faceless alien to his house, knowing from the CSM that Dr. Openshaw had died that evening. (00:15:10)
Plot hole: The subject of the stakeout - the religious man dressed as a female prostitute to 'put the other prostitutes at ease' before trying to 'save' them - is shown when Scully is on the phone telling Mulder about it; the man has a very masculine face, a hairy stomach and is in no way convincing. It's extremely unlikely that such an obvious cross-dressed male would fool such a large amount of people.